Structural analysis of linear and conformational epitopes of allergens

Regul Toxicol Pharmacol. 2009 Aug;54(3 Suppl):S11-9. doi: 10.1016/j.yrtph.2008.11.007. Epub 2008 Dec 14.


In many countries regulatory agencies have adopted safety guidelines, based on bioinformatics rules from the WHO/FAO and EFSA recommendations, to prevent potentially allergenic novel foods or agricultural products from reaching consumers. We created the Structural Database of Allergenic Proteins (SDAP, to combine data that had previously been available only as flat files on Web pages or in the literature. SDAP was designed to be user friendly, to be of maximum use to regulatory agencies, clinicians, as well as to scientists interested in assessing the potential allergenic risk of a protein. We developed methods, unique to SDAP, to compare the physicochemical properties of discrete areas of allergenic proteins to known IgE epitopes. We developed a new similarity measure, the property distance (PD) value that can be used to detect related segments in allergens with clinical observed cross-reactivity. We have now expanded this work to obtain experimental validation of the PD index as a quantitative predictor of IgE cross-reactivity, by designing peptide variants with predetermined PD scores relative to known IgE epitopes. In complementary work we show how sequence motifs characteristic of allergenic proteins in protein families can be used as fingerprints for allergenicity.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.
  • Review

MeSH terms

  • Allergens / chemistry
  • Allergens / classification
  • Allergens / immunology*
  • Amino Acid Motifs
  • Amino Acid Sequence
  • Databases, Protein
  • Epitopes / chemistry*
  • Molecular Sequence Data
  • Protein Conformation
  • Proteins / immunology*
  • World Health Organization


  • Allergens
  • Epitopes
  • Proteins